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Bratusek, a former prime minister is under investigation at home for conflict of interest as she appointed herself as commissioner nominee while still in office.

She was slated to become one of Juncker's seven senior commissioners, in charge of the nascent 'energy union'.

Earlier on Wednesday, Juncker's spokeswoman Natasha Bertaud defended her and "strongly denied" reports that Bratusek had withdrawn her candidacy.

According to an EU source, the new commission chief felt it was unfair to treat her differently than other commissioners who were questioned twice or got a second legal opinion on their declaration of financial interests.

Juncker may try and play hardball with the European Parliament, who can only vote down the entire commission.

But MEPs who were part of the discussions with Juncker doubt he will continue to back her after the negative vote Wednesday evening.

"I don't think Juncker will stick to her. There was a clear vote against her. It wasn't even so much about the nomination process, but her performance here in the committee, the fact that she didn't know the basics, not even news articles. We gave her 20 hours to draw her own conclusions, she didn't, so now she's history," German Socialist MEP Matthias Groote told this website.

If Juncker decides not to risk his entire team over Bratusek, he will ask the Slovenian government for a new name, which will have to be confirmed by member states before being sent to the EP with the job description.

One name doing the rounds in Violeta Bulc, a recently-appointed minister for "development, strategic projects and Cohesion" who describes herself on her blog as a believer "in the power of networks, holistic individual, and positive energy."

Juncker may also tweak portfolios or swap some commissioners, depending on whom Ljubljana decides to send.

Up for discussion is the Hungarian commissioner's job description after MEPs said Tibor Navracsics could be a member of the commission but not in charge of education, culture and citizenship. The citizenship part may be instead be given to his Greek colleague, who is in charge of migration and home affairs.

There are also talks with the Socialists about another controversial commissioner - Spain's Miguel Arias Canete. Juncker agreed to broaden the portfolio of Frans Timmermans, a vice-president for better regulation. Under his new job description, Timmermans will also be in charge of "sustainable development", which means he will also oversee Canete, who is commissioner for energy and climate.

Canete sparked the outrage of green MEPs and activists, as he was a shareholder in two oil companies just days before the hearings. He sold those shares and so did his wife and son, but his brother-in-law took over his family's interests.

A legal opinion on Monday, requested by the energy and environment MEPs, said Canete could take on the job.

He passed the vote on Wednesday with 83 votes to 42, and his portfolio by 77 to 48.

Four other commissioners - all with economic portfolios who were part of a political chess game in case Canete fell also sailed through on Wednesday: France's Pierre Moscovici, Britain's Jonathan Hill, Latvia's Valdis Dombrovskis and Finland's Jyrki Katainen.

Opinion

We must not undervalue what a massive step the European Parliament vote represents. The hard work has paid off. We can take a moment to celebrate, but the hard work begins again for finalising strong protection for European whistleblowers.